research papers
Acta Crystallographica Section C
catalyst-reduction step of the cross-coupling. Reductive
elimination would then give rise to the observed dimer.
Although only a minor impurity in the isolated desired
product, by-product (I) was the sole species identified during
single-crystal structure determination. Whilst impurities from
cross-coupling reactions can occur, this study demonstrates
the importance of reconciling the crystal structures from cross-
coupling reactions with the identity of the material in the bulk
product.
Structural Chemistry
ISSN 2053-2296
0
2
,2 -Bi[benzo[b]thiophene]: an
unexpected isolation of the
benzo[b]thiophene dimer
a
b
Eugene Y. Cheung, * Lewis D. Pennington, Michael D.
b
c
Bartberger and Richard J. Staples
a
b
Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA, Amgen Inc., One
c
Amgen Center Drive, Thousand Oaks, CA 91320, USA, and Department of
Chemistry and Chemical Biology, Chemistry Building, Michigan State University,
East Lansing, MI 48824, USA
Received 8 April 2014
Accepted 26 April 2014
2
. Experimental
0
2.1. Synthesis and crystallization
The crystal structure of 2,2 -bi[benzo[b]thiophene], C H S ,
10 2
16
at 173 K has triclinic (P1) symmetry. It is of interest with
respect to its apparent mode of synthesis, as it is a by-product
of a Stille cross-coupling reaction in which it was not explictly
detected by spectroscopic methods. It was upon crystal
structure analysis of a specimen isolated from the mother
liquor that this reaction was determined to give rise to the title
compound, which is a dimer arising from the starting material.
Two independent half-molecules of this dimer comprise the
asymmetric unit, and the full molecules are generated via
inversion centers. Both molecules in the unit cell exhibit ring
disorder, and they are essentially identical because of their
rigidity and planarity.
Compound (I) was synthesized using a one-step procedure
starting from (benzo[b]thiophen-2-yl)tributylstannane (3.0 g,
7
(
4
.1 mmol) and dichloridobis(triphenylphosphane)palladium(II)
0.33 g, 0.47 mmol). 2-Chloro-3-methylpyridine (0.60 g,
.7 mmol), while present in the reaction mixture (9.4 ml
tetrahydrofuran, reflux, 43 h), did not participate in the di-
merization reaction.
After completion of the cross-coupling reaction, as deter-
mined by high-performance liquid chromatography–mass
spectroscopy (HPLC–MS), the reaction mixture was adsorbed
onto silica gel and subjected to flash chromatography (19:1
hexane–ethyl acetate). The isolated material was re-subjected
to silica-gel flash chromatography (19:1 hexane–ethyl acetate)
Keywords: crystal structures; chemical reactions and
mechanisms; computational chemistry; pharmaceutical
compounds; structure and spectroscopy; by-products.
to remove residual undesired by-products (e.g. Bu SnX resi-
3
dues). A portion of the purified material (48 mg of 1.0 g, 94%
1
yield, >95% purity by HPLC–MS and H NMR) was dissolved
in diisopropyl ether (1.0 ml) and the resulting solution was
filtered through a 0.45 mm Teflon filter into an uncapped small
vial, which was then placed into a large vial containing hexane
(4.0 ml). Vapor diffusion led to the crystallization of a cluster
of solid, of which one crystal appeared to be suitable for
single-crystal X-ray diffraction analysis. Although the solid
was colorless, the selected crystal was clearer than its
surroundings.
1
. Introduction
This account of the structural chemistry of 2,2 -bi[benzo-
b]thiophene], (I), is of a rather serendipitous nature. The
0
[
original intent was to utilize (benzo[b]thiophen-2-yl)tributyl-
stannane in a Stille cross-coupling reaction (Espinet &
Echavarren, 2004) with 2-chloro-3-methylpyridine to yield
1
2-(benzo[b]thiophen-2-yl)-3-methylpyridine. Surprisingly, analy-
With regard to the H NMR spectroscopic data, a very small
sis of the crystals that were grown and harvested after the
reaction did not support the structure of the desired
compound, but rather that of (I), which is a by-product formed
during the cross-coupling reaction. The generalized cross-
aberrant singlet was noted in the aromatic region, and if this
tiny peak is assumed to be that of a single proton of compound
(I), then (I) was present at less than 3 mol% in solution,
perhaps even as low as 2 mol%. The elusiveness of (I) in
solution is further established by its total lack of appearance in
the HPLC–MS data. However, once the unexpected X-ray
crystal structure was obtained, re-evaluation of the bulk
material in a deliberate search for this by-product by thin-
layer chromatography (TLC) revealed traces of it.
2
coupling reaction involves a halogenated sp -hybridized
2
0
species R reacting with an sp -hybridized species R that is
bonded to a sterically hindered metal core. In order for
homodimer (I) to form, the species benzo[b]thiophene–Pd–
II
0
benzo[b]thiophene must have formed during the Pd to Pd
Acta Cryst. (2014). C70, 547–549
doi:10.1107/S2053229614009401
# 2014 International Union of Crystallography 547